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Renaming VariantAnnotator SnpEff keys 

This is to head off potential confusion with the output from the SnpEff tool itself,
which also uses a key named EFF.
This commit is contained in:
David Roazen 2011-09-15 16:09:07 -04:00
parent 1971fb35d7
commit d78e00e5b2
4 changed files with 53 additions and 45 deletions
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90
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java
View File

@ -68,23 +68,31 @@ public class SnpEff extends InfoFieldAnnotation implements ExperimentalAnnotatio
// Key names for the INFO field annotations we will add to each record, along
// with parsing-related information:
public enum InfoFieldKey {
EFF (-1),
EFF_IMPACT (0),
EFF_CODON_CHANGE (1),
EFF_AMINO_ACID_CHANGE (2),
EFF_GENE_NAME (3),
EFF_GENE_BIOTYPE (4),
EFF_TRANSCRIPT_ID (6),
EFF_EXON_ID (7);
EFFECT_KEY ("SNPEFF_EFFECT", -1),
IMPACT_KEY ("SNPEFF_IMPACT", 0),
CODON_CHANGE_KEY ("SNPEFF_CODON_CHANGE", 1),
AMINO_ACID_CHANGE_KEY ("SNPEFF_AMINO_ACID_CHANGE", 2),
GENE_NAME_KEY ("SNPEFF_GENE_NAME", 3),
GENE_BIOTYPE_KEY ("SNPEFF_GENE_BIOTYPE", 4),
TRANSCRIPT_ID_KEY ("SNPEFF_TRANSCRIPT_ID", 6),
EXON_ID_KEY ("SNPEFF_EXON_ID", 7);
// Actual text of the key
private final String keyName;
// Index within the effect metadata subfields from the SnpEff EFF annotation
// where each key's associated value can be found during parsing.
private final int fieldIndex;
InfoFieldKey ( int fieldIndex ) {
InfoFieldKey ( String keyName, int fieldIndex ) {
this.keyName = keyName;
this.fieldIndex = fieldIndex;
}
public String getKeyName() {
return keyName;
}
public int getFieldIndex() {
return fieldIndex;
}
@ -292,27 +300,27 @@ public class SnpEff extends InfoFieldAnnotation implements ExperimentalAnnotatio
}
public List<String> getKeyNames() {
return Arrays.asList( InfoFieldKey.EFF.toString(),
InfoFieldKey.EFF_IMPACT.toString(),
InfoFieldKey.EFF_CODON_CHANGE.toString(),
InfoFieldKey.EFF_AMINO_ACID_CHANGE.toString(),
InfoFieldKey.EFF_GENE_NAME.toString(),
InfoFieldKey.EFF_GENE_BIOTYPE.toString(),
InfoFieldKey.EFF_TRANSCRIPT_ID.toString(),
InfoFieldKey.EFF_EXON_ID.toString()
return Arrays.asList( InfoFieldKey.EFFECT_KEY.getKeyName(),
InfoFieldKey.IMPACT_KEY.getKeyName(),
InfoFieldKey.CODON_CHANGE_KEY.getKeyName(),
InfoFieldKey.AMINO_ACID_CHANGE_KEY.getKeyName(),
InfoFieldKey.GENE_NAME_KEY.getKeyName(),
InfoFieldKey.GENE_BIOTYPE_KEY.getKeyName(),
InfoFieldKey.TRANSCRIPT_ID_KEY.getKeyName(),
InfoFieldKey.EXON_ID_KEY.getKeyName()
);
}
public List<VCFInfoHeaderLine> getDescriptions() {
return Arrays.asList(
new VCFInfoHeaderLine(InfoFieldKey.EFF.toString(), 1, VCFHeaderLineType.String, "The highest-impact effect resulting from the current variant (or one of the highest-impact effects, if there is a tie)"),
new VCFInfoHeaderLine(InfoFieldKey.EFF_IMPACT.toString(), 1, VCFHeaderLineType.String, "Impact of the highest-impact effect resulting from the current variant " + Arrays.toString(EffectImpact.values())),
new VCFInfoHeaderLine(InfoFieldKey.EFF_CODON_CHANGE.toString(), 1, VCFHeaderLineType.String, "Old/New codon for the highest-impact effect resulting from the current variant"),
new VCFInfoHeaderLine(InfoFieldKey.EFF_AMINO_ACID_CHANGE.toString(), 1, VCFHeaderLineType.String, "Old/New amino acid for the highest-impact effect resulting from the current variant"),
new VCFInfoHeaderLine(InfoFieldKey.EFF_GENE_NAME.toString(), 1, VCFHeaderLineType.String, "Gene name for the highest-impact effect resulting from the current variant"),
new VCFInfoHeaderLine(InfoFieldKey.EFF_GENE_BIOTYPE.toString(), 1, VCFHeaderLineType.String, "Gene biotype for the highest-impact effect resulting from the current variant"),
new VCFInfoHeaderLine(InfoFieldKey.EFF_TRANSCRIPT_ID.toString(), 1, VCFHeaderLineType.String, "Transcript ID for the highest-impact effect resulting from the current variant"),
new VCFInfoHeaderLine(InfoFieldKey.EFF_EXON_ID.toString(), 1, VCFHeaderLineType.String, "Exon ID for the highest-impact effect resulting from the current variant")
new VCFInfoHeaderLine(InfoFieldKey.EFFECT_KEY.getKeyName(), 1, VCFHeaderLineType.String, "The highest-impact effect resulting from the current variant (or one of the highest-impact effects, if there is a tie)"),
new VCFInfoHeaderLine(InfoFieldKey.IMPACT_KEY.getKeyName(), 1, VCFHeaderLineType.String, "Impact of the highest-impact effect resulting from the current variant " + Arrays.toString(EffectImpact.values())),
new VCFInfoHeaderLine(InfoFieldKey.CODON_CHANGE_KEY.getKeyName(), 1, VCFHeaderLineType.String, "Old/New codon for the highest-impact effect resulting from the current variant"),
new VCFInfoHeaderLine(InfoFieldKey.AMINO_ACID_CHANGE_KEY.getKeyName(), 1, VCFHeaderLineType.String, "Old/New amino acid for the highest-impact effect resulting from the current variant"),
new VCFInfoHeaderLine(InfoFieldKey.GENE_NAME_KEY.getKeyName(), 1, VCFHeaderLineType.String, "Gene name for the highest-impact effect resulting from the current variant"),
new VCFInfoHeaderLine(InfoFieldKey.GENE_BIOTYPE_KEY.getKeyName(), 1, VCFHeaderLineType.String, "Gene biotype for the highest-impact effect resulting from the current variant"),
new VCFInfoHeaderLine(InfoFieldKey.TRANSCRIPT_ID_KEY.getKeyName(), 1, VCFHeaderLineType.String, "Transcript ID for the highest-impact effect resulting from the current variant"),
new VCFInfoHeaderLine(InfoFieldKey.EXON_ID_KEY.getKeyName(), 1, VCFHeaderLineType.String, "Exon ID for the highest-impact effect resulting from the current variant")
);
}
@ -375,16 +383,16 @@ public class SnpEff extends InfoFieldAnnotation implements ExperimentalAnnotatio
}
try {
impact = EffectImpact.valueOf(effectMetadata[InfoFieldKey.EFF_IMPACT.getFieldIndex()]);
impact = EffectImpact.valueOf(effectMetadata[InfoFieldKey.IMPACT_KEY.getFieldIndex()]);
}
catch ( IllegalArgumentException e ) {
parseError(String.format("Unrecognized value for effect impact: %s", effectMetadata[InfoFieldKey.EFF_IMPACT.getFieldIndex()]));
parseError(String.format("Unrecognized value for effect impact: %s", effectMetadata[InfoFieldKey.IMPACT_KEY.getFieldIndex()]));
}
codonChange = effectMetadata[InfoFieldKey.EFF_CODON_CHANGE.getFieldIndex()];
aminoAcidChange = effectMetadata[InfoFieldKey.EFF_AMINO_ACID_CHANGE.getFieldIndex()];
geneName = effectMetadata[InfoFieldKey.EFF_GENE_NAME.getFieldIndex()];
geneBiotype = effectMetadata[InfoFieldKey.EFF_GENE_BIOTYPE.getFieldIndex()];
codonChange = effectMetadata[InfoFieldKey.CODON_CHANGE_KEY.getFieldIndex()];
aminoAcidChange = effectMetadata[InfoFieldKey.AMINO_ACID_CHANGE_KEY.getFieldIndex()];
geneName = effectMetadata[InfoFieldKey.GENE_NAME_KEY.getFieldIndex()];
geneBiotype = effectMetadata[InfoFieldKey.GENE_BIOTYPE_KEY.getFieldIndex()];
if ( effectMetadata[SNPEFF_CODING_FIELD_INDEX].trim().length() > 0 ) {
try {
@ -398,8 +406,8 @@ public class SnpEff extends InfoFieldAnnotation implements ExperimentalAnnotatio
coding = EffectCoding.UNKNOWN;
}
transcriptID = effectMetadata[InfoFieldKey.EFF_TRANSCRIPT_ID.getFieldIndex()];
exonID = effectMetadata[InfoFieldKey.EFF_EXON_ID.getFieldIndex()];
transcriptID = effectMetadata[InfoFieldKey.TRANSCRIPT_ID_KEY.getFieldIndex()];
exonID = effectMetadata[InfoFieldKey.EXON_ID_KEY.getFieldIndex()];
}
private void parseError ( String message ) {
@ -443,14 +451,14 @@ public class SnpEff extends InfoFieldAnnotation implements ExperimentalAnnotatio
public Map<String, Object> getAnnotations() {
Map<String, Object> annotations = new LinkedHashMap<String, Object>(Utils.optimumHashSize(InfoFieldKey.values().length));
addAnnotation(annotations, InfoFieldKey.EFF.toString(), effect.toString());
addAnnotation(annotations, InfoFieldKey.EFF_IMPACT.toString(), impact.toString());
addAnnotation(annotations, InfoFieldKey.EFF_CODON_CHANGE.toString(), codonChange);
addAnnotation(annotations, InfoFieldKey.EFF_AMINO_ACID_CHANGE.toString(), aminoAcidChange);
addAnnotation(annotations, InfoFieldKey.EFF_GENE_NAME.toString(), geneName);
addAnnotation(annotations, InfoFieldKey.EFF_GENE_BIOTYPE.toString(), geneBiotype);
addAnnotation(annotations, InfoFieldKey.EFF_TRANSCRIPT_ID.toString(), transcriptID);
addAnnotation(annotations, InfoFieldKey.EFF_EXON_ID.toString(), exonID);
addAnnotation(annotations, InfoFieldKey.EFFECT_KEY.getKeyName(), effect.toString());
addAnnotation(annotations, InfoFieldKey.IMPACT_KEY.getKeyName(), impact.toString());
addAnnotation(annotations, InfoFieldKey.CODON_CHANGE_KEY.getKeyName(), codonChange);
addAnnotation(annotations, InfoFieldKey.AMINO_ACID_CHANGE_KEY.getKeyName(), aminoAcidChange);
addAnnotation(annotations, InfoFieldKey.GENE_NAME_KEY.getKeyName(), geneName);
addAnnotation(annotations, InfoFieldKey.GENE_BIOTYPE_KEY.getKeyName(), geneBiotype);
addAnnotation(annotations, InfoFieldKey.TRANSCRIPT_ID_KEY.getKeyName(), transcriptID);
addAnnotation(annotations, InfoFieldKey.EXON_ID_KEY.getKeyName(), exonID);
return annotations;
}

4
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java
View File

@ -62,8 +62,8 @@ public class FunctionalClass extends VariantStratifier {
annotationId++;
} while (eval.hasAttribute(key));
} else if ( eval.hasAttribute(SnpEff.InfoFieldKey.EFF.name() ) ) {
SnpEff.EffectType snpEffType = SnpEff.EffectType.valueOf(eval.getAttribute(SnpEff.InfoFieldKey.EFF.name()).toString());
} else if ( eval.hasAttribute(SnpEff.InfoFieldKey.EFFECT_KEY.getKeyName() ) ) {
SnpEff.EffectType snpEffType = SnpEff.EffectType.valueOf(eval.getAttribute(SnpEff.InfoFieldKey.EFFECT_KEY.getKeyName()).toString());
if ( snpEffType == SnpEff.EffectType.STOP_GAINED )
type = FunctionalType.nonsense;
else if ( snpEffType == SnpEff.EffectType.NON_SYNONYMOUS_CODING )

2
public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
View File

@ -134,7 +134,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
validationDataLocation + "1kg_exomes_unfiltered.AFR.unfiltered.vcf --snpEffFile " + validationDataLocation +
"snpEff.AFR.unfiltered.vcf -L 1:1-1,500,000",
1,
Arrays.asList("a1c3ba9efc28ee0606339604095076ea")
Arrays.asList("486fc6a5ca1819f5ab180d5d72b1ebc9")
);
executeTest("Testing SnpEff annotations", spec);
}

2
public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
View File

@ -32,7 +32,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
1,
Arrays.asList("f5f811ceb973d7fd6c1b2b734f1b2b12")
);
executeTest("testStratifySamplesAndExcludeMonomorphicSites", spec);
executeTest("testFunctionClassWithSnpeff", spec);
}
@Test